Dual perspective: Pelagic and benthic communities as biological and functional indicators in riverine ecosystems

Microbial communities are widely recognised as rapid and sensitive indicators of environmental change, yet they remain underutilised in biomonitoring despite their potential to complement or surpass traditional bioindicators. Conventional biomonitoring approaches in freshwater ecosystems typically rely on fish, macroinvertebrates or plants, each constrained by practical and ecological limitations that restrict when, where and how they can be used to assess ecosystems. In contrast, microbial communities provide both taxonomic and functional signals that reflect a wide range of processes, including direct links to water chemistry. Here, we evaluate microbial communities as environmental indicators of river ecosystem health. We sampled both pelagic and benthic microbial communities across space and time, integrating community composition and ecosystem function. Microbial assemblages differed significantly between the sampled fractions (pelagic vs benthic) and seasonally. Using threshold indicator analyses, we identified a broad set of genera with association to water chemistry and ecosystem function. However, there was no consistent indicator taxa based on these environmental gradients or ecosystem function across sample fraction or season. This highlights the high responsiveness of microbial communities to environmental gradients and temporal change. While context-specific indicators show clear potential, developing robust microbial metrics will require accounting for benthic and pelagic habitats and seasonal variability inherent in riverine ecosystems.